A conventional light microscope provides a resolution on the order of about 250 nanometers in a lateral two-dimensional (“2D”) plane (i.e., x-y plane) and on the order of about 600 nanometers, or worse, in an axial direction (i.e., z axis). To obtain higher resolution images, other microscopy methods must be utilized.
4Pi-Microscopy
A number of techniques have been able to provide a higher resolution in the axial direction to achieve an improved 3D image of structures. For example, 4Pi confocal microscopy and I5M microscopy can provide a resolution on the order of about 250 nanometers in the lateral plane (same as conventional microscopy) and on the order of about 100 nanometers in the axial direction (approximately 6-fold higher resolution in the axial direction than conventional microscopy).
4Pi-microscopy is a fluorescence far-field technique that enhances the diffraction-limited optical resolution of confocal laser scanning microscopy in the axial direction by utilizing two opposing objectives. For example, 4Pi-microscopy is described in an article titled “Fundamental improvement of resolution with a 4Pi-confocal fluorescence microscope using two-photon exciation” by S. Hell and E. H. K. Stelzer (1992, Opt. Comm. 93: 277-282), which is incorporated herein by reference in its entirety. A coherent superposition of two counter-propagating wavefronts at a common focus point modulates an axially elongated focus of a single objective resulting in a sharp central maximum and two axially shifted side-maxima. By applying 2-photon excitation (“2PE”), the side-maxima height can be lowered and the artifacts produced by the side-maxima can be removed by post-processing, resulting in 3D imaging with an axial resolution of 100 to 150 nanometers. A more detailed description of the 2PE is described in an article titled “Two-photon laser scanning fluorescence microscopy,” by W. Denk, J. H. Strickler, and W. W. Webb (1990, Science 248, 73-76), which is incorporated herein by reference in its entirety.
I5M is a “wide-field version” of 4Pi that can utilize a spatially incoherent light source, e.g., a mercury lamp, and a CCD camera instead of a confocal scanner in the same kind of interference geometry. While the high I5M side-maxima are often difficult to remove, localization measurements of single particles can be performed more quickly. For example, I5M microscopy is described in an article titled “I5M: 3D widefield light microscopy with better than 100 nm axial resolution” by M. G. L. Gustafsson, D. A. Agard, and J. W. Sedat (1999, J. Microsc. 195: 10-16), which is incorporated herein by reference in its entirety.
A “Type C” mode of 4Pi microscopy, which increases 4Pi-resolution by 30% down to about 100 nanometers, is also the base for implementation of I5M into current 4Pi microscopes. A more detailed description of this 4Pi microscopy is described in an article titled “Cooperative 4Pi excitation and detection yields 7-fold sharper optical sections in live cell microscopy” by H. Gugel, J. Bewersdorf, S. Jakobs, J. Engelhardt, R. Storz, and S. W. Hell (2004, Biophys. J. 87, 4146-4152), which is incorporated herein by reference in its entirety. 4Pi Type C imaging recently identified histone H2AX structures, with improvements in imaging resolution that enabled the definition of boundaries of γ-H2AX spreading based on their size and distribution. A more detailed description of these improvements is included in an article titled “Novel H2AX Chromatin Structures Revealed by 4Pi Microscopy,” by J. Bewersdorf, B. T. Bennett, and K. L. Knight (2006, Proc. Nat. Acad. Sci., doi:10.1073/pnas.0608709103), which is incorporated herein by reference in its entirety.
Fluorescence Photoactivation Microscopy (FPALM)
A further improvement in the lateral resolution has been achieved by utilizing Fluorescence Photo Activation Localization Microscopy (“FPALM”). Specifically, FPALM imaging techniques can be utilized to facilitate visualization of multiple structures down to about a demonstrated 30 nanometer length scale (and smaller in principle) in the cell nucleus. Thus, FPALM provides nearly a one order of magnitude higher resolution in the lateral plane than conventional, 4Pi, or I5M microscopy. However, a problem with current FPALM imaging techniques is that it does not provide improved 3D resolution in the axial direction. Although FPALM can provide a 3D image of a particle by combining images of multiple 2D planes of a sample, this type of image has only a very poor resolution in the axial direction comparable to conventional microscopy because it fails to provide any axial resolution within any of the combined images. In other words, FPALM can only image a structure that can be observed in a particular slice of a sample, i.e., within a particular 2D plane of the sample, with improved resolution. FPALM cannot identify any fine structure along the axial direction of the particular slice.
Thus, FPALM has not yet been extended to 3D imaging. This is due to the currently used standard widefield or total internal reflection (TIR) microscopy geometries not being suitable to 3D FPALM imaging.
FPALM measures the positions (by localization) of large numbers (e.g., 104 to 106) of single fluorescent molecules to generate images with nanometer resolution (demonstrated resolution 20-30 nanometers). FPALM is predicated on single molecule detection methods that allow position localization of spatially isolated fluorophores with much higher precision than the theoretical resolution limit of a light microscope.
The key to high resolution FPALM is the activation of only a sparse subset of available fluorescent probes at any one time, such that nearly all fluorophores are spatially separated by at least the optical resolution of the system and can be localized individually. The molecules are generally localized using single molecule detection methods. Fluorescent probes, such as photoactivatable green fluorescent protein (“PA-GFP”), are initially in a non-fluorescent or weakly fluorescent state. A more detailed description of some fluorescent probes is provided in an article titled “A photoactiavatable GFP for selective photolabeling of proteins and cells,” by G. H. Patterson and J. Lippincott-Schwarz (2002, Science 297, 1873-1877), which is incorporated herein by reference in its entirety. Wide-field irradiation with a short wavelength (˜405 nanometers) source activates a stochastic, sparse subset of the fluorophores (irreversibly in the case of PA-GFP) in the field of view. The activated molecules are then excited as for normal single molecule fluorescence using a longer wavelength (˜480 to 500 nanometers) source, and then imaged with a sensitive CCD camera until photobleached. Photobleaching may be actively induced, or may occur spontaneously after a certain number of fluorophore excitation-emission cycles. This process is repeated until the entire probe population is exhausted, or until sufficient information about the sample has been obtained. The positions of observed and localized molecules are then plotted to construct a 2D map.
The resolution in FPALM is referred to as a localization-based resolution, in contrast to the diffraction-limited optical resolution of conventional microscopes. While the localization-based resolution is approximately proportional to the optical resolution of the microscope, it can exceed the optical resolution by a large factor (e.g., more than a factor of 10) if a sufficient number of photons is collected per fluorescent molecule. A more detailed description of the localization-based resolution is provided in an article titled “Precise Nanometer Localization Analysis for Individual Fluorescent Probes,” by R. E. Thompson, D. R. Larson, and W. W. Webb (2002, Biophys. J. 82: 2775-2783), which is incorporated herein by reference in its entirety.
Thus, there is a need for improved ultra high 3D resolution in fluorescence microscopy. None of the current fluorescence microscopy techniques can enhance resolutions of light microscopy to levels of electron microscopy. A need exists for a fluorescence microscopy technique that can resolve particles in 3D with a resolution higher than the current resolution of 100 nanometers in 4Pi fluorescence microscopy. The present invention is directed to satisfying one or more of these needs and solving other problems.